Job ID = 2162386 sra ファイルのダウンロード中... Completed: 750585K bytes transferred in 11 seconds (552550K bits/sec), in 3 files, 4 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 36218 0 36218 0 0 48652 0 --:--:-- --:--:-- --:--:-- 65493 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 5537830 spots for /home/okishinya/chipatlas/results/dm3/SRX066245/SRR222073.sra Written 5537830 spots total Written 18552417 spots for /home/okishinya/chipatlas/results/dm3/SRX066245/SRR222072.sra Written 18552417 spots total Written 19852318 spots for /home/okishinya/chipatlas/results/dm3/SRX066245/SRR222074.sra Written 19852318 spots total fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:01 43942565 reads; of these: 43942565 (100.00%) were unpaired; of these: 16211672 (36.89%) aligned 0 times 20354226 (46.32%) aligned exactly 1 time 7376667 (16.79%) aligned >1 times 63.11% overall alignment rate Time searching: 00:11:02 Overall time: 00:11:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 19529741 / 27730893 = 0.7043 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Tue, 21 Apr 2015 13:55:57: # Command line: callpeak -t SRX066245.bam -f BAM -g dm -n SRX066245.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX066245.20 # format = BAM # ChIP-seq file = ['SRX066245.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Tue, 21 Apr 2015 13:55:57: # Command line: callpeak -t SRX066245.bam -f BAM -g dm -n SRX066245.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX066245.05 # format = BAM # ChIP-seq file = ['SRX066245.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Tue, 21 Apr 2015 13:55:57: # Command line: callpeak -t SRX066245.bam -f BAM -g dm -n SRX066245.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX066245.10 # format = BAM # ChIP-seq file = ['SRX066245.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Tue, 21 Apr 2015 13:55:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:55:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:55:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:55:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:55:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:55:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:56:03: 1000000 INFO @ Tue, 21 Apr 2015 13:56:03: 1000000 INFO @ Tue, 21 Apr 2015 13:56:03: 1000000 INFO @ Tue, 21 Apr 2015 13:56:09: 2000000 INFO @ Tue, 21 Apr 2015 13:56:09: 2000000 INFO @ Tue, 21 Apr 2015 13:56:09: 2000000 INFO @ Tue, 21 Apr 2015 13:56:15: 3000000 INFO @ Tue, 21 Apr 2015 13:56:15: 3000000 INFO @ Tue, 21 Apr 2015 13:56:15: 3000000 INFO @ Tue, 21 Apr 2015 13:56:20: 4000000 INFO @ Tue, 21 Apr 2015 13:56:20: 4000000 INFO @ Tue, 21 Apr 2015 13:56:20: 4000000 INFO @ Tue, 21 Apr 2015 13:56:26: 5000000 INFO @ Tue, 21 Apr 2015 13:56:26: 5000000 INFO @ Tue, 21 Apr 2015 13:56:26: 5000000 INFO @ Tue, 21 Apr 2015 13:56:31: 6000000 INFO @ Tue, 21 Apr 2015 13:56:31: 6000000 INFO @ Tue, 21 Apr 2015 13:56:32: 6000000 INFO @ Tue, 21 Apr 2015 13:56:36: 7000000 INFO @ Tue, 21 Apr 2015 13:56:36: 7000000 INFO @ Tue, 21 Apr 2015 13:56:37: 7000000 INFO @ Tue, 21 Apr 2015 13:56:41: 8000000 INFO @ Tue, 21 Apr 2015 13:56:41: 8000000 INFO @ Tue, 21 Apr 2015 13:56:42: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:56:42: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:56:42: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:56:42: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:56:42: #1 total tags in treatment: 8201152 INFO @ Tue, 21 Apr 2015 13:56:42: #1 total tags in treatment: 8201152 INFO @ Tue, 21 Apr 2015 13:56:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:56:42: 8000000 INFO @ Tue, 21 Apr 2015 13:56:44: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 13:56:44: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 13:56:44: #1 total tags in treatment: 8201152 INFO @ Tue, 21 Apr 2015 13:56:44: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:56:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:56:44: #1 tags after filtering in treatment: 8199078 INFO @ Tue, 21 Apr 2015 13:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:56:44: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:44: #1 tags after filtering in treatment: 8199078 INFO @ Tue, 21 Apr 2015 13:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:56:44: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:45: #1 tags after filtering in treatment: 8199078 INFO @ Tue, 21 Apr 2015 13:56:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:56:45: #1 finished! INFO @ Tue, 21 Apr 2015 13:56:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:56:46: #2 number of paired peaks: 864 WARNING @ Tue, 21 Apr 2015 13:56:46: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Tue, 21 Apr 2015 13:56:46: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:46: #2 number of paired peaks: 864 WARNING @ Tue, 21 Apr 2015 13:56:46: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Tue, 21 Apr 2015 13:56:46: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:47: #2 number of paired peaks: 864 WARNING @ Tue, 21 Apr 2015 13:56:47: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Tue, 21 Apr 2015 13:56:47: start model_add_line... INFO @ Tue, 21 Apr 2015 13:56:50: start X-correlation... INFO @ Tue, 21 Apr 2015 13:56:50: end of X-cor INFO @ Tue, 21 Apr 2015 13:56:50: #2 finished! INFO @ Tue, 21 Apr 2015 13:56:50: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 13:56:50: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 13:56:50: #2.2 Generate R script for model : SRX066245.20_model.r WARNING @ Tue, 21 Apr 2015 13:56:50: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:56:50: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 13:56:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:56:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:56:50: start X-correlation... INFO @ Tue, 21 Apr 2015 13:56:50: end of X-cor INFO @ Tue, 21 Apr 2015 13:56:50: #2 finished! INFO @ Tue, 21 Apr 2015 13:56:50: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 13:56:50: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 13:56:50: #2.2 Generate R script for model : SRX066245.05_model.r WARNING @ Tue, 21 Apr 2015 13:56:50: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:56:50: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 13:56:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:56:50: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:56:51: start X-correlation... INFO @ Tue, 21 Apr 2015 13:56:51: end of X-cor INFO @ Tue, 21 Apr 2015 13:56:51: #2 finished! INFO @ Tue, 21 Apr 2015 13:56:51: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 13:56:51: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 13:56:51: #2.2 Generate R script for model : SRX066245.10_model.r WARNING @ Tue, 21 Apr 2015 13:56:51: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:56:51: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 13:56:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:56:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:57:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:57:36: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:57:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:58:07: #4 Write output xls file... SRX066245.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:58:07: #4 Write peak in narrowPeak format file... SRX066245.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:58:07: #4 Write summits bed file... SRX066245.20_summits.bed INFO @ Tue, 21 Apr 2015 13:58:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (963 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:58:07: #4 Write output xls file... SRX066245.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:58:08: #4 Write peak in narrowPeak format file... SRX066245.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:58:08: #4 Write summits bed file... SRX066245.10_summits.bed INFO @ Tue, 21 Apr 2015 13:58:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1653 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write output xls file... SRX066245.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:58:16: #4 Write peak in narrowPeak format file... SRX066245.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:58:17: #4 Write summits bed file... SRX066245.05_summits.bed INFO @ Tue, 21 Apr 2015 13:58:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3557 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。